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- PDB-1c6y: ALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT H... -

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Basic information

Entry
Database: PDB / ID: 1c6y
TitleALTERNATE BINDING SITE FOR THE P1-P3 GROUP OF A CLASS OF POTENT HIV-1 PROTEASE INHIBITORS AS A RESULT OF CONCERTED STRUCTURAL CHANGE IN 80'S LOOP.
ComponentsPROTEIN (PROTEASE)
KeywordsHYDROLASE
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMunshi, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: An alternate binding site for the P1-P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease.
Authors: Munshi, S. / Chen, Z. / Yan, Y. / Li, Y. / Olsen, D.B. / Schock, H.B. / Galvin, B.B. / Dorsey, B. / Kuo, L.C.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Crystal Structure at 1.9-A Resolution of Human Immunodeficiency Virus (HIV) II Protease Complexed with L-735,524, an Orally Bioavailable Inhibitor of the HIV Proteases
Authors: Chen, Z. / Li, Y. / Chen, E. / Hall, D.L. / Darke, P.L. / Culberson, C. / Shafer, J.A. / Kuo, L.C.
History
DepositionDec 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (PROTEASE)
B: PROTEIN (PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2173
Polymers21,6032
Non-polymers6141
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-21 kcal/mol
Surface area9560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.44, 88.26, 42.94
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (PROTEASE)


Mass: 10801.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NY5 ISOLATE / Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: NY5 ISOLATE / Production host: Escherichia coli (E. coli)
References: UniProt: O09893, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-MK1 / N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE / INDINAVIR


Mass: 613.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H47N5O4 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL) ...L-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO] -4(S)-HYDROXY-2(R)-PHENYLMETHLPENTANAMIDE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growDetails: THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD. 9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T THERE IS ONE PROTEASE ...Details: THE CRYSTAL WAS PREPARED WITH CO CRYSTALLIZATION METHOD. 9X MUTANT PROTEASE HAS NINE POINT MUTATIONS COMPARED TO WILD TYPE: L10V,K20M,L24I,S37D,M46I,I54V,L63P,A71V,V82T THERE IS ONE PROTEASE DIMER IN AN ASYMMETRICAL UNIT. THE TWO MOLECULES ARE LABELED AS CHAIN A AND CHAIN B. THERE IS ONE L-735,524 INHIBITOR MOLECULE LABELED AS MK1.
Crystal grow
*PLUS
pH: 5 / Method: other
Details: inhibitor-protein mixture and the reservoir solution were mixed in a 1:1(v/v) ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14-6 mg/mlenzyme1drop
210 mMMES1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
53 mM1dropNaN3
70.6-0.8 M1reservoirNaCl
80.1 M1reservoirNaOAc
6inhibitor1dropmixed with the protein containing buffer in a molar ratio of 1:3 to 1:5, with a final DMSO concentration of 2-5%

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. all: 35099 / Num. obs: 7254 / % possible obs: 89 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.5→2.59 Å / % possible all: 84
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 35099
Reflection shell
*PLUS
% possible obs: 84 % / Num. unique obs: 676 / Num. measured obs: 1775 / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 4.4

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→8 Å / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.18 / Rfactor obs: 0.18 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 45 84 1643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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